


Why Did You Leave?

by Mid_Nightmare



Category: Marvel, Marvel Cinematic Universe, Spider-Man (Tom Holland Movies), The Avengers (Marvel Movies)
Genre: A/B/O, ABO dynamics, Age Difference, Alpha Tony, Alpha Tony Stark, Alpha/Beta/Omega Dynamics, Alpha/Omega, Alternate Universe - Canon Divergence, Anal, Anal Fingering, Anal Sex, Angst, Angst and Hurt/Comfort, Angst with a Happy Ending, Background Relationships, Canon Divergence - Post-Captain America: Civil War (Movie), Claiming Bites, Consensual Underage Sex, Happy Ending, Hurt Peter, Hurt Tony Stark, Implied Mpreg, Implied Relationships, Implied Sexual Content, Implied/Referenced Underage Sex, Knotting, M/M, Mating, Mating Bites, Mating Bond, Mating Cycles/In Heat, Mating Rituals, Mpreg, Non-Traditional Alpha/Beta/Omega Dynamics, Omega Peter, Omega Peter Parker, Original Character(s), Post Mpreg, Post-Captain America: Civil War (Movie), Post-Civil War (Marvel), References to Knotting, Romance, Scent Marking, Scenting, Soul Bond, Teen Angst, Teen Pregnancy, Teenagers, True Mates, Underage Kissing, Underage Sex, Unplanned Pregnancy
Language: English
Status: In-Progress
Published: 2019-08-02
Updated: 2019-08-02
Packaged: 2020-07-10 11:50:02
Rating: Explicit
Warnings: Underage
Chapters: 1
Words: 4,658
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/19905247
Author URL: https://archiveofourown.org/users/Mid_Nightmare/pseuds/Mid_Nightmare
Summary: Everyone knew that teenagers were known to be a bit dramatic. Peter Parker didn’t think he was one of those teens. Yeah, he certainly suffered some abnormal things for kids his age, but he never thought he was being dramatic when he complained about his problems. But right now, he was literally sitting on the floor of his bathroom holding something in his hand that could entirely change his life.~*~Peter finds out at the ripe age of sixteen that he is pregnant with his alpha's pup. Too scared to tell Tony, he runs away and abandons his old life. Follow him through his journey of hiding from his mate and raising his pups as the world around him crumbles.





	Why Did You Leave?

**Author's Note:**

> Hello!  
> My first chaptered Starker story is almost complete, and I found this little gem hiding in my drafts, so I thought I'd bring it back out to play! This story will be set Post-Civil War and Post-SpiderMan Homecoming, but it will span through to Endgame.  
> Get ready for a bumpy ride!  
> Much love <3

Everyone knows that teenagers are known to be a bit dramatic. Peter Parker didn’t think he was one of those teens. Yeah, he certainly suffered some abnormal things for kids his age, but he never thought he was being  _ dramatic _ when he complained about his problems. But right now, he was literally sitting on the floor of his bathroom holding something in his hand that could entirely change his life.

And no, Peter Benjamin Parker was not over-exaggerating because fuck you, this stupid little white stick was going to tell him whether or not the best night of his life was about to make him suffer massive consequences.

As he set the stick on the edge of his sink, he leaned his head back against the cabinet, sighing softly as he fought the tears coming to his eyes. Why…  _ Why  _ did the best thing that ever happened to him be the thing that was going to ruin him? When the first tear slid down his cheek, the dams keeping his memories at bay broke.

  
  


_ “Happy birthday,” a slightly gruff but familiar voice called from behind him. Whipping around, Peter had the widest smile on his lips, the corners of his eyes crinkling just slightly as he reached out for the alpha. _

_ “Tony,” he whispered with pure joy and excitement filling his words. Tony returned the smile and gently held onto the narrow hips of the teenager before brushing his lips against the other’s. _

_ A chuckle rumbled from deep within the older man’s chest, and he lightly rested his forehead against the omega’s. “I thought I told you to be ready for our date at six,” he teased as his smile morphed to a playful smirk. As a flush spread across the younger’s cheeks, a small giggle left him as he pecked the bottom lip of the alpha. _

_ “Tony, it’s five-thirty. I still have thirty minutes to finish getting ready.” With the softest scoff and a playful roll of his eyes, Tony leaned in and stole a real kiss from the other, slotting their lips together gently while the fingers of one hand slipped into the soft curls on the back of the other’s neck. _

_ Peter melted into the kiss, pressing up against his lover’s chest and tightening his arms around Tony’s neck. He whimpered as the alpha pulled back just enough that even with all of Peter’s stretching, their lips could only lightly brush against one another’s. “Then get ready, sugarplum.” The whisper had a shiver running up the youth’s spine, and a faint flush dusted his cheeks before he gave a small nod. His lips puckered in a silent beg for another kiss, and he was given his reward before Tony slipped out of his arms and walked in the opposite direction. “Twenty-seven minutes! Don’t be late,” he smirked, winking at the younger over his shoulder. _

_ Taking a moment to enjoy watching the other leave, the blushing youth ran up the stairs towards Tony’s - could he call it his now? - room to change. In exactly twenty-four and a half minutes, Peter was coming down the main staircase in a perfectly fitted slate gray suit. His tie was a deep burgundy red, the perfect shade of Tony’s IronMan suit. He beamed as he saw a cherry red tie in his own shade of Spider-Man red around his partner’s neck. _

_ “You look beautiful as always,” Tony hummed before taking Peter’s hand in his and gently pressing his lips to his knuckles. He smiled as he got the shy reaction that he absolutely loved from his partner along with a sweet peck. “Let’s go, sugarplum. I got surprises waiting for you.” _

  
  


Peter jumped as his phone buzzed against his thigh, slamming his head accidentally against the metal handle of the cabinet. “Fuck!” he hissed as he rubbed the spot before looking down at his phone. His stomach twisted in knots as he saw that it was a text from Tony.

He chewed on his lip before looking at the message. Even in his turmoil, the sound of the alpha’s voice filled his head as he read.  _ Can I take you to dinner tonight, beautiful? Spend the night or the weekend back home? _

Peter knew for a fact that by home Tony was referring to his penthouse because ever since they started dating, home was with Tony.  _ I'd love to. Time? _ He sent back before staring at the wall, trying to swallow down the butterflies that were returning. He glanced at his phone to see he still had another few minutes to wait before he let out another groan. He hated waiting.

_ I'll be there at 5:30. _ Peter nodded to himself at the text before sending back a confirmation text of his own. “Only two more minutes to go…” he whispered to himself. It felt like the longest two minutes of his life, but he tried to not think about it too much until Karen’s soft and familiar voice spoke from his earpiece.

“Peter?” she started softly, and even though he knew it was coming, he still jumped. “I apologize for startling you, but your timer is finished.” Peter nodded slightly, whispering a thank you to the AI before reaching his hand above his head.

His fingers curled around the small plastic, and suddenly he felt the butterflies fly up and catch in his throat again. He wanted to vomit from the nerves, especially as the butterflies rose and tickled the back of his throat. He tried to push them down, tried to take in a deep breath, but they still persisted. His eyes slipped closed as he pulled the stick down and held it for a moment, trying to steady his breath. “I can do this. I can do this,” he whispered to himself.

When his eyes opened, he knew instantly that he could  _ not _ do this. There on the screen were two little pink lines, and at that moment, Peter had never hated the color pink so much in his entire life. A sudden sobbed clawed its way out of his throat. Hiding his face in his hands, the tears that Peter had been trying desperately to not let out came flowing down his cheeks in massive rivers. The stick was clutched so tightly in his hand that it snapped, and the pain of the plastic suddenly stabbing into his hand was nothing compared to the pain of his heart.

It felt like the world was spinning, and Peter suddenly couldn’t tell what was up and what was down. He tossed the stick into the trash before curling into himself, hugging his knees to his chest and sobbing into his jeans. “I don’t know what to do. I don’t know what to  _ do _ ,” he whispered to himself over and over like a mantra.

“Peter?” Karen called softly in his ear, and it shouldn’t be possible for an AI - a computer - to sound like it cared so much, and yet here he was crying on his bathroom floor and feeling as though an AI was trying to comfort him. “I’ve detected that your heart rate is elevated and your oxygen intake is a bit low. Is there anything I can do to help?”

He took a couple of lungfuls of air in small gasps before sighing softly. “I’m… I’m alri- Actually, I’m not. Karen… Can you find me an omega clinic?”

“Of course, Peter,” she answered. “Do you wish to go to the one that Mr. Stark recommended? With the high discretion and the background in studying mutants?”

Peter sniffled, originally wanting to say no, but what if his mutation because of the spider was causing a false positive? What if there was something wrong that was just throwing off his pH? “Yes, please. Make an appointment for as soon as possible,” he requested. He couldn’t be too certain, and maybe if they really did value discretion, he could keep this from Tony until he figured it out.

He thought about asking Karen to run a scan on him, but then he remembered that Tony had access to those files, and he could easily stumble across something the teen didn’t want him to find. So he quickly abandoned that idea.

He wiped his cheeks and eyes before grabbing some toilet paper to blow his nose. He shook his head before hiding all of the evidence of his at-home test and trying to calm his shaky hands. “Peter? I’ve contacted the clinic, and they can see you in an hour and twenty minutes. Would you like me to contact Happy for a ride?”

“No!” he cried quickly before forcing himself to relax. “I’m sorry, Karen, but I can’t tell anyone. Not yet. I’ll just take the train or-or walk.”

“I understand, Peter. Please let me know if there is anything I can do.” His frown deepened. Her voice sounded so worried and sad, and he was nervous that he had upset her as ridiculous as that seemed. She was the only one he was willing to let help him right now, and he needed her now more than ever.

“Will.. you give me directions to the clinic?” he asked nervously, hoping that maybe if she did this, it would help her feel better.

Her voice seems to perk up a bit as she agreed, and she immediately began to give him directions. He asked her to wait just long enough for him to grab a few things, and once he was out the door, he allowed her to start up again. They walked until Peter hopped onto the train. It was going to be a long ride, so he listened to her carefully for the exit she told him to take. After the better part of an hour, Peter found himself walking into the clinic.

It was not what he was expecting. He thought it’d feel like a hospital, but it actually was quite warm and comfortable when he passed through their front doors. The walls were a creamy white color, and there were dark wood accents filling the room.

He walked up to the front desk where a kind, smiling woman looked up at him. “Mr. Parker?” she asked, and he nodded a bit timidly at her. “Don’t worry, Mr. Parker. We take excellent care of our clients. Any information that is shared with the doctor or within this clinic will remain only here.”

He nodded again; “Thank you. I… Is there any paperwork I need to fill out?” He asked instead of his other question. He was going to save that one for the doctor if the answer he feared was true.

“Actually, yes. Your previous information has already been sent to us, but there are still a few things for you to fill out.” She then gathered a few papers, marking them up and showing Peter what information he needed to sign and fill out. Before he left, however, she did ask one question. “The doctor will be with you shortly, once you’ve finished, but I do need the reason for your visit.”

Peter swallowed, hanging his head and hiding his eyes behind his curls. “Um… Pregnancy test,” he whispered, and when he chanced a glance at her, she had a sympathetic smile.

“I will include that in the note for the doctor, and I will put you into our most discreet section of cases. Nothing discussed with the doctor and no test results will be shared with anyone besides you. Including your mate,” she added after catching a glimpse of the healed mark on the side of his neck.

His hand came up to cover it shyly as his cheeks turned red in a blush. He felt better knowing that nothing would be shared, not even with Tony. He’d never want the man to find out why he was here if not from him. Feeling a little more at ease, he thanked the woman sincerely before sitting in a chair and working on the paperwork. It only took a few minutes, and when he returned it to her, she smiled more genuinely at him than before.

He was still shy as he waited for the doctor, but his knee was bouncing a little less than it had on the train. It was only a minute later when a nurse came out to get him. She led him back into a room where his vitals were checked, and then she had him sit while she drew some blood to run some tests. He talked quietly to her, trying to distract himself. It looked a bit more like a clinic now that he was in the room, but even this was a bit warmer than the standard white on white.

He ended up sitting on the bed for a bit, swinging his feet and softly talking to Karen. She sounded very pleased now that he seemed more relaxed, and he was happy to hear her sounding more like herself. After a while, there was a soft knock on the door before in walked a kind-looking middle-aged woman. Her light blonde hair was pulled up into a bun, and her white coat was open to reveal more casual clothing underneath.

“Hello, Mr. Parker,” she said with a gentle warmth. He suddenly felt at ease talking to her after realizing she was an omega as well, and he smiled his first true smile all day. She returned the gesture before shaking one of his hands gently. “My name is Dr. Sarah Summers. I’ll be the doctor seeing you today, and if you’d like, I can be your continuing care doctor. We've started your blood tests. Everything is normal as of right now, but we did notice a few abnormalities. Are you aware of what this clinic specializes in?” she asked kindly.

“Um... I heard that you actually, uh, you, um, deal with mutants and people with ‘special powers’?” It sounded ridiculous coming out the way he'd said it, but he wasn’t sure how to explain it any other way.

She chuckled softly as she took her seat in front of the computer and began to type and log in. “Yes, that’s one way to put it. Are you aware of these abnormalities?” she asked, looking over at him with kind eyes.

He was always nervous to talk about these things, but she made him feel so comfortable and safe, and if she couldn’t say anything… “I was bitten by a radioactive spider when I was 13. I didn’t notice the effects right away, but within a few months, I did. I had turned 14 and suddenly, even though I’m… small, I could do a lot of things I couldn’t do before.”

She nodded as he talked, typing things into the computer. “Do you mind telling me a few of these things? I would like to get a better idea of your enhancements, and if you would consent to it, I’d like to have your blood sent to the lab for further testing just to make sure that there isn’t anything hiding or anything that could be developing.”

He nodded quietly. “I understand, and that’s alright. But um, as for, uh, abilities. I can stop a bus with my bare hands. I have more strength and agility than before. I’m a bit faster as well plus I can walk on walls and various surfaces with an enhanced grip on my feet and hands. I have something that my mate refers to as ‘Spidey-Senses’. My hair will stand up when there’s something coming, and I just get a general feeling.”

She listed everything in his chart and hummed softly before nodding. “That’s all very interesting. It appears you were given spider-like traits. I will have some of your blood sent to the lab just to make sure those are the only enhancements, and that nothing else is manifesting.” She continued to type for a moment before turning back to face him. “Now, when did you present as an omega?”

He blushed faintly, tucking his chin and hiding his eyes behind his curly bangs. “When I was 14, shortly after the bite. It happened about a week after my birthday.” She nodded, and he heard the typing of keys again.

“And when did you mate with your partner?” His cheeks burned even brighter, and he reached up to touch the healed bite on the left side of his neck. He hadn’t realized before that it had been exposed the entire time thanks to the Johnny he was wearing.

“My sixteenth birthday,” he whispered nervously, playing with his fingers.

“And you’ve consummated your relationship?”

“Yes,” he squeaked softly, his voice breaking on the word. She smiled over at him before gently patting his knee in a way that distinctly reminded him of Aunt May.

“And I know that you’re here for a pregnancy test. Would he be the father?” she asked gently.

He looked up at that, and even though his cheeks were burning, he didn’t want her to doubt him at all or to think that he was uncertain in this idea. “Yes. He’s the only one I've been with.”

She nodded and smiled kindly at him. “Perfect. I just had to check, of course.” He nodded back, understanding her questioning, but now that she’s mention why he’s here, he suddenly felt the nerves creeping up again. He went to speak, but she gently spoke first. “I do not have the results yet. It should only be a few more minutes. Is your partner aware of the fact you may be pregnant?”

He shook his head gently before looking down at his hands in his lap. “No… I took an at-home test today, and it came back positive, but I wasn’t sure. I didn’t want to tell him if I wasn’t sure…” She nodded and gently patted his knee again. 

“I understand. You should talk to him however even if it is negative. You should be using protection if you are not ready for children.” She sounded a little like a mother scolding her child, and it caused a faint smile to pull at his lips as he nodded. “Good. If it’s negative, I’ll write you a prescription for birth control and suppressants as well to help.”

“Thank you, Doctor Summers.” He said sincerely, smiling at her. She returned the smile before typing a few more things into the computer. Once she was finished with her typing, she returned her full attention to him.

“You’re due for your routine physical. Would you like to get that done while we wait for your test results? It should only take a few moments.”

“Okay,” he agreed before following her directions. In less than ten minutes, his physical was complete, and Dr. Summers had managed to leave such a joyful imprint that he told her when she returned to her desk that he would like to continue his care under her.

“I’m glad that I can continue to help you, Mr. Parker.”

“You can call me Peter,” he said shyly with a wide smile.

She smiled back, agreeing quietly before a knock at the door caught both of their attentions. “Come in,” she called, and the nurse from before came into the room with a small folder, handing it to the doctor before slipping out of the room. Dr. Summers opened the folder and began to look at the paperwork inside, humming softly. Peter watched her, and when he caught her eyes stop and appear to read the same section again, his stomach sank. She closed the folder and set it on her keyboard before turning her body and attention to the youth sitting on the bed.

Before she could even say anything, Peter spoke, his voice shaken as he realized it must be true. “It’s positive, isn’t it?”

Dr. Summers smiled sadly at the boy before nodding slightly. When she heard the soft sniffle, she reached out and gently took the boy’s hands in hers. “I’m sorry, Peter. If there is anything I can do to help, please call the clinic. Since I am an omega doctor, I can help you through the pregnancy and can even recommend a pediatrician once the baby is born. But if you should choose that this isn’t what you want-”

“I’m not getting rid of the baby,” he whispered frantically, looking up at her as tears slid down his cheeks. “I can’t get rid of my baby.” The pain in his words was reflected in his eyes, and she frowned slightly before nodding.

“I understand. I merely wanted to inform you of all your options.” He nodded before pulling one of his hands free to wipe away his tears.

“Thank you,” he whispered, sniffling softly.

She nodded and pulled away for a moment to retrieve a tissue for the boy. She handed it over to him while giving his own hand a small squeeze. “If there is anything you need, please do call,” she said again.

He nodded once more and wiped his eyes before blowing his nose, looking for a trash can to throw his tissue away. “I will, promise,” he said as he gently tossed his tissue into the container. When he turned back to her, his fingers were fidgeting with the hem of his Johnny. “Can… you tell at all how far along?” he asked a little nervously. He wanted to know if it really did come from what he feared it did.

“It’s hard to tell,” she admitted, looking back at the notes, “given the results though, I’d say a few weeks, about four?”

He sniffled again, a small hiccup caused him to jump slightly. “Of course,” he mumbled softly to himself, but apparently she heard him.

“The night of your mating?” she asked gently, having glanced at the screen to see that Peter’s birthday was twenty-five days ago. He had mentioned that he had mated with his partner on his sixteenth birthday, so it seemed possible that this was an effect because of it.

He nodded slightly, looking down at his lap. “Best night of my life,” he mumbled as his ears turned pink. She smiled faintly and chuckled before shaking her head slowly.

“Should you ever need any help adjusting, there are parenting classes that you and your mate can attend,” she added.

He frowned as Tony returned to his mind. He was nervous about telling the other man, but he figured that maybe the parenting classes would help. He nodded, thanked Dr. Summers one last time, and once they agreed that there was nothing else for this appointment and that Peter would receive a call about his other test results, she left. He quickly changed back into his clothes, checked everything over once again to make sure he hadn’t lost anything, before walking back to the front desk.

The woman behind the counter smiled kindly at him, and when he went to pay, she told him it had already been handled. His brows furrowed in confusion as he pressed, but Karen quietly spoke in his ear. “I used your card earlier to pay for your appointment. If Mr. Stark asks, I would recommend telling him that you merely needed a physical.”

He smiled at the care of the AI before wishing a good day to the woman behind the counter. He took a card with Dr. Summer’s information before leaving, heading outside and back into the fresh air. “Karen, what time is it?”

“It is currently three twenty-seven. You have two hours and three minutes before Mr. Stark plans to arrive.”

“Do you know where he plans to take me?” he asked as he began to walk down the street. He managed to be in a much higher-end part of Manhattan somehow. That certainly explained the long train ride...

“I do not know, but I can ask Friday.”

“Perfect. I just need to know if it’s fancy enough that I need to change clothes.”

“Of course, Peter,” she said tenderly. He walked around and waited, looking around the stores lining the street. He almost wanted to go shopping, but he absolutely hated spending Tony’s money no matter how much the man pushed. The alpha gave him a credit card on his birthday, and yet he still barely ever touched it. “Friday has informed me that Mr. Stark plans to take you to a ‘secret location’.”

He sighed softly, but before he could say anything, his phone rang with a phone call. “Mr. Stark is on the line,” Karen told him, and Peter’s stomach flipped nervously.

“Answer it,” he said gently, and suddenly the tension in his body immediately evaporated as Tony’s voice filled his ear.

“What are you doing in Manhattan?” he asked curiously.

“Well hello to you too, alpha,” he chuckled before wandering into a random store. He has time to kill, might as well look. “And I went to that omega clinic you recommended. I needed a check-up, and I hadn’t gotten around to it yet.”

Tony hummed softly on his line, and Peter smiled as he could picture the man casually stroking his jaw while thinking of the omega’s words. “Well, that is true. Haven’t been since before your birthday after all,” and the smirk was obvious as was Peter’s blush.

“Yeah, so I figured I had time, so I went.”

“Got it. And now you’re standing in one of the most expensive shops in all of Manhattan?” Tony teased. Peter’s blush got darker. He didn’t know that when he wandered in.

“I was only wandering in to look. I’ll leave.”

“No, baby, stay. You need something nice to wear tonight. Why don’t you get a suit and I’ll pick you up in the Manhattan area? Buy yourself something pretty while you’re at it.”

Peter chewed on his lip before glancing down at his worn tee-shirt and ripped jeans. “I really can’t wear jeans and a tee-shirt?”

“Absolutely not. Also, you need a suit, baby. What if I want to show you off at the next gala?” Tony teased.

“I have a suit.”

“You can never have too many suits.”

Peter groaned softly, shaking his head. “You know I hate spending your money…”

“And you know I love spoiling you. So go buy a suit, make sure it fits, and send anything you don’t want to carry to the house. Buy yourself something pretty while you’re out, okay? I’ll see you soon, Oma.”

“Okay, alpha,” he whispered shyly.

“Good boy. I love you, see you soon.”

“I love you too.” Peter quietly pocketed his phone, cheeks still burning, and once he was off the line, a young man approached him. The man gave him a quick once over, seeming to hang up on his very tattered street clothes, but he said nothing except the standard greeting and asked what Peter’s looking for.

It took a little while to find something that he liked enough, but he agreed to the solid black suit with the red button-up and a gold tie. He actually got a few extra shirts, a soft pink and a deep purple that he thought Tony would like on him, and went to checkout. Peter asked to have the suit held there for another few hours since he was going to be back to change into them, and the man agreed after he paid for his purchases. He ignored the price entirely to save himself from getting sick because he really,  _ really _ hated spending money.

He headed outside afterward, still a bit bored, but trying to find something fun to do. “Mr. Stark asked me to remind you to get something pretty for yourself,” Karen spoke suddenly.

“I don’t even know what he means by that,” he grumbled softly before catching sight of a store. He stared for a few seconds before realizing exactly what Tony meant. He sighed softly to himself before stepping into the store. Something special for himself, more like something special for Tony.


End file.
